[gmx-users] Filling box with long linear molecules

Mark Abraham mark.j.abraham at gmail.com
Mon Apr 24 11:04:43 CEST 2017


Not really. The general problem of filling space in a tight packing is
hard. Usable approaches include decreasing the VDW radius while inserting
molecules, using gmx genconf to start from an initially crystalline
configuration of suitable density that is then equilibrated for a long
time, using a much larger simulation cell that will later have its volume
reduced via pressure coupling, or dedicated software like
http://www.ime.unicamp.br/~martinez/packmol/home.shtml and various membrane


On Mon, Apr 24, 2017 at 10:46 AM Kamps, M. <m.kamps at student.rug.nl> wrote:

> Dear GMX users,
> I am working with polymers (~20 carbon atoms) in an enclosed box. In
> order to fill this box with polymers, I currently use an iteration of
> multiple steps.
> Currently, the polymers are created via an external code, and the
> resulting polymers are linear strings of polymers, with only a
> 'zig-zag' motion at the carbon atoms. Currently I am filling this box
> via the 'gmx insert-molecules -nmol X' command, where it will try to
> fill the box.
> Due to the orientation of the polymers, the box is considered full and
> GROMACS cannot add any more polymers. However, after performing a
> small relaxation the polymers will 'bend and twist' all around each
> other, resulting in lots of empty space. This process is repeated
> several times until gmx insert-molecules can no longer fit any more
> polymers in the box.
> My question, is there a more efficient way to do this? Can GROMACS
> insert-molecules while 'bending' the polymers?
> Kind regards,
> Mark
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